The Indonesian government has threatened to deploy its navy and air force against a group of Australian protesters planning to sail from Queensland to the controversial province of West Papua.

From President Susilo Bambang Yudhoyono down, Indonesia is interpreting the protest as an Australian attack on Indonesia's sovereignty over the independence-minded area, as the issue threatens to blow up into a significant diplomatic incident.

The Indonesian Co-ordinating Minister for Political, Legal and Security, Djoko Suyanto, confirmed on Sunday he had ordered that jet fighters and navy vessels be prepared to intercept the boats, and has also made his feelings clear to Australian ambassador Greg Moriarty.

The so-called Freedom Flotilla, which is planning to sale from Queensland to West Papua. Photo: Svea Ess

"I have asked the navy and air force to standby and anticipate their journey," he said in a statement to the Jakarta Post newspaper.

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He had told the Australian ambassador: "There should be no nation allowing its soil to be used as a departure point for the movement of a group aimed at disturbing other nation's sovereignty. That is very clear."

Mr Yudhoyono's spokesman Teuku Faizasyah said any facilitation by Australia "won't be good for our bilateral relationships". They come on top of comments from the president directly last week saying Western governments should prevent any political activity that disturbed good relations.

Members of the Freedom Flotilla to West Papua. Photo: Svea Ess

Indonesian foreign affairs spokesman Marty Natalegawa said Indonesia "always respected the sovereignty and territorial integrity of other countries", saying he hoped "the same principal is reciprocated", and adding the country would "act decisively" against any threat.

The so-called "Freedom Flotilla" is now in Cooktown in North Queensland, readying itself to sail north. Two boats carrying about 50 West Papuan and indigenous Australian protesters aims to land in Papua New Guinea, then cross the land border into Merauke, West Papua, in early September. However, flotilla spokesman Ruben Blake said this timetable was "flexible" because "some of the sailors are still learning what to do".

They are travelling on Aboriginal passports and West Papuan visas, neither of which is internationally recognised.

The Freedom Flotilla says it will continue as planned despite the Indonesian government's threats of navy and air force intervention.

"We come in peace," Uncle Kevin Buzzacott said on Monday.

Freedom Flotilla co-founder Jacob Rumbiak said the Indonesian government's "heavy-handed response" prompted the question: "Why are they scared? If we share concerns for human rights abuses and violence that are going on in Papua then they have nothing to fear from our mission."

One of the protesters is Amos Wainggai, who helped create the last large diplomatic rift between Australia and Indonesia when he was one of a group of 42 West Papuans who came to Australia by boat in 2006 and was later granted asylum.

A spokesman for the Foreign Minister Bob Carr said there was nothing the Australian government could do to stop an otherwise legal boat sailing from an Australian port. Once they were in Indonesian waters, however, they were subject to that country's laws.

He added that the protesters were perpetrating a "cruel hoax" on the people of West Papua if they gave them the impression that other countries supported independence from Indonesia.

Shadow foreign affairs spokesman Julie Bishop supported Indonesia's right to deploy the military against the flotilla: "If this freedom flotilla breaches Indonesia's territorial sovereignty, Indonesia is entitled to use whatever means it wishes to protect it.

"Indonesia is within its rights to turn these boats around where it is safe to do so."

Flotilla spokesman Mr Blake chose to focus on another comment by Mr Djoko, that Indonesia shared the group's concerns about "human rights and violence in the Papuan region".

"We think that's a positive ... and if that's true, we have a solid basis of dialogue."

He said the flotilla was "an opportunity for our leaders to take a solid stance on the issue rather than talking".

No other issue is as sensitive in Indonesia as the question of West Papua. Despite Australian guaranteeing Indonesia's "territorial integrity" in the Lombok Treaty of 2006, it's widely believed in Jakarta, even among the political elite, that Australia is secretly working towards West Papuan independence. Australia is still blamed in Jakarta for East Timor's break away.

Influential Indonesian politician Hajriyanto Thohari drew the link in May, urging his countrymen not to believe the assurances of Western nations of Indonesian sovereignty over the province.

"The West is always like that, you can't trust them completely," he said.